The river is part of the water basin of Lake Eyasi.

The Wembere River originates in hilly country in central Tanzania at 6.0º south, and flows northwards through a branch of the Eastern Rift Valley.

Its tributary the Nyahua River forms a seasonal floodplain 60 miles long and 1-5 km wide, covering 11,000 ha.

The floodplain consists of flooded grasslands, inundated during the wet season and laced with drainage channels.

Below the floodplain the river turns northeast and empties into the south end of Lake Kitangiri.